Due to its enormous benefits, the research and industry communities have shown an increasing interest in the Microservices Architecture (MSA) style over the last few years. Despite this, there is a limited evidence-based and thorough understanding of the types of issues (e.g., faults, errors, failures, mistakes) faced by microservices system developers and causes that trigger the issues. Such evidence-based understanding of issues and causes is vital for longterm, impactful, and quality research and practice in the MSA style. To that end, we conducted an empirical study on 1,345 issue discussions extracted from five open source microservices systems hosted on GitHub. Our analysis led to the first of its kind taxonomy of the types of issues in open source microservices systems, informing that the problems originating from Technical debt (321, 23.86%), Build (145, 10.78%), Security (137, 10.18%), and Service execution and communication (119, 8.84%) are prominent. We identified that “General programming errors”, “Poor security management”, “Invalid configuration and communication”, and “Legacy versions, compatibility and dependency” are the predominant causes for the leading four issue categories. Study results streamline a taxonomy of issues, their mapping with underlying causes, and present empirical findings that could facilitate research and development on emerging and next-generation microservices systems.